The companies announced a pilot program to run XenApp on Amazon’s Elastic Compute Cloud service Thursday.

“Virtualizing applications provides IT managers a single instance of each application in either the data center or the cloud (i.e., EC2),” Citrix CTO Simon Crosby writes in a blog post. “Applications are then delivered via application streaming directly to Windows devices for both online and offline use.”

The pilot will let Citrix customers move their XenApp licenses from their own data centers to Amazon EC2 and “run their applications in a fully supported environment,” Citrix says. However, eligibility is restricted to Citrix customers who are also members of Amazon’s Windows Server License Mobility Pilot, which allows migration of Windows Server licenses to Amazon EC2.

The XenApp/Amazon pilot also does not yet support Amazon’s Virtual Private Cloud, which is designed to bring enterprise-class security to computing resources that run in Amazon’s data centers.

“Citrix is continuing to work with Amazon on plans to incorporate VPC into the Citrix Pilot at a future date,” Citrix says.The pilot is therefore of limited use today, but potentially interesting to businesses considering whether to eventually offload internal IT infrastructure to a cloud provider. With XenApp running in Amazon EC2, a business could substantially reduce the number of physical servers it has to manage.

Crosby admits that customers often complain today’s clouds aren’t “enterprise class,” and have concerns about availability and security. But he argues that cloud services are maturing quickly and offer many advantages that can’t be replicated in a typical enterprise data center.

On Amazon, “With a single API call you can create a 1TB SQL database that has a 15 day, up to the second granularity of transactional roll-back, that is continually backed up and available,” Crosby writes. “And all you have to do is pay for compute and storage. Why on earth would you not write an app on that? Well, if your app is tied to your existing enterprise database, then you’re stuck, but otherwise, you’d be silly not to.”

Crosby adds that “the extensive use of automation in the cloud in general makes them far less susceptible to the traditional issues of the enterprise: human misconfiguration errors.”

Customers still must carefully evaluate infrastructure-as-a-service clouds to make sure a particular application can be supported, he writes.

“What matters most is to evaluate the capability set of a particular IaaS cloud vendor, and map it to the requirements of your enterprise applications,” Crosby states. “Can the IaaS feature set support the application? That’s what you need to answer first. Then you can decide if the quality of that feature set is ‘enterprise class’.”